Mahmoud Moradi

Free-Energy and Molecular Dynamics Analysis of Ser195 and Thr195 Rotameric States in Thrombin

This study uses molecular dynamics simulations to compare the conformational energetics of Ser195 and Thr195 in thrombin, revealing differences in rotameric states and their impact on catalytic geometry.

Differential Behavior of Uncleaved gp160 Human Immunodeficiency Virus Type 1 (HIV-1) Envelope (Env) Glycoproteins

This study uses molecular dynamics simulations to show that two structures of uncleaved HIV-1 Env, assigned to the same conformational state, exhibit distinct dynamic behaviors.

Dimer opening enables brain-type creatine kinase to sense membrane curvature

This study identifies dimer opening in CK-BB as a mechanism for sensing membrane curvature and regulating ATP regeneration under acidic conditions and substrate binding.

Cholesterol-Dependent Structure and Dynamics of Curved Lipid Vesicles Revealed by Dry MARTINI Simulations

This study uses Dry MARTINI simulations to investigate how cholesterol affects the structure and dynamics of curved lipid vesicles, finding increased membrane thickness and altered lipid behavior with higher cholesterol concentrations.

Interplay Between Cholesterol Concentration and Membrane Curvature in Liposomes Revealed by Molecular Dynamics Simulations

This study uses molecular dynamics simulations to show how cholesterol concentration and membrane curvature affect the structure and dynamics of liposomes composed of DOPC and cholesterol.

Predicting Binding Affinities for the Binding Domain of Hyperpolarization-Activated Cyclic Nucleotide-Gated Channel Isoforms Using Free-Energy Perturbation

The paper uses free-energy perturbation to calculate binding affinities of cAMP to HCN isoforms 1-4 CNBDs, revealing differences in channel activation sensitivity.

An Investigation of the Conformational Dynamics of ABC Exporter PCAT1 using Microsecond-Level MD Simulations

This study uses microsecond MD simulations and FEP to analyze nucleotide binding and conformational dynamics of PCAT1, revealing Mg2+ and substrate-dependent stabilization mechanisms.

Characterizing the Conformational Dynamics of an Intrinsically Disordered Localization Sequence

This study examines how single-residue substitutions in a mitochondrial localization peptide affect its conformational dynamics, revealing that sequence changes can bias structural ensembles and influence targeting efficiency.

Structural dynamics of sphingosine kinase 1 regulation and inhibition

This study identifies structural dynamics and regulatory mechanisms of SK1, revealing a novel inhibitory paradigm and insights for therapeutic development.

Lipid-Mediated Modulation of mGluR2 Embedded in Micelle and Bilayer Environments: Insights from Molecular Dynamics

This study uses molecular dynamics simulations to show that CHS concentration affects mGluR2's structural stability and conformational dynamics in micelle and bilayer environments.

Molecular Insights into Cholesterol Concentration Effects on Planar and Curved Lipid Bilayers for Liposomal Drug Delivery

This study uses molecular dynamics simulations to investigate how cholesterol affects planar and curved lipid bilayers, revealing geometry-dependent structural and dynamic changes.

Molecular dynamics investigation of the influenza hemagglutinin conformational changes in acidic pH

This study uses molecular dynamics simulations to investigate how protonation affects the conformational changes of influenza hemagglutinin at low pH, revealing structural shifts linked to receptor binding and immune evasion.

Conformational Transition Pathways in Major Facilitator Superfamily Transporters

This study uses molecular dynamics simulations to compare conformational transitions in MFS transporters, finding similar mechanisms across classes with some functional differences.

Differential Behavior of Conformational Dynamics in Active and Inactive States of Cannabinoid Receptor 1

This study uses molecular dynamics simulations to compare conformational dynamics of inactive and active states of CB1 receptor, identifying key structural differences and electrostatic interactions that influence its function.

Lipid-dependent conformational dynamics of bacterial ATP-binding cassette transporter Sav1866

The paper investigates how lipid environments affect the conformational dynamics of the bacterial ABC transporter Sav1866 using molecular dynamics simulations.

Cholesterol Dependence on the Conformational Changes of Metabotropic Glutamate Receptor 1

This study uses molecular dynamics simulations to show that cholesterol modulates conformational changes in mGluR1 dimers, with 10% cholesterol causing the most significant effects.